scholarly journals Transcription Factors and MicroRNA Interplay: A New Strategy for Crop Improvement

2018 ◽  
Author(s):  
Sumit Jangra ◽  
Vrantika Chaudhary ◽  
Neelam R. Yadav
Keyword(s):  
Transcription Factors ◽  
Crop Improvement ◽  
New Strategy

scholarly journals Transcriptional profiling of gametogenesis in the green seaweed Ulva mutabilis identifies an RWP‐RK transcription factors linked to reproduction

2021 ◽  
Author(s):  
Xiaojie Liu ◽  
Jonas Blomme ◽  
Kenny Bogaert ◽  
Sofie D’hondt ◽  
Thomas Wichard ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Sexual Reproduction ◽  
Higher Plants ◽  
Crop Improvement ◽  
Functional Characterization ◽  
Land Plants ◽  
Alternative Source ◽  
Starting Point ◽  
Green Seaweed

Abstract Background The molecular mechanism underlying sexual reproduction in land plants is well understood in model plants and is a target for crop improvement. However, unlike land plants, the genetic basis involved in triggering reproduction and gamete formation remains elusive in most seaweeds, which are increasingly viewed as an alternative source of functional food and feedstock for energy applications. Results Gametogenesis of Ulva mutabilis, a model organism for green seaweeds, is studied. We analyze transcriptome dynamics at different time points during gametogenesis following induction of reproduction by fragmentation and removal of sporulation inhibitors. Analyses demonstrate that 45% of the genes in the genome are differentially expressed during gametogenesis. We identified several transcription factors that potentially play a key role in the early gametogenesis of Ulva given the function of their homologs in higher plants and microalgae. In particular, the detailed expression pattern of an evolutionary conserved transcription factor containing an RWP-RK domain suggests a key role during Ulva gametogenesis. Conclusions Transcriptomic analyses of gametogenesis in the green seaweed Ulva highlight the importance of a conserved RWP-RK transcription factor in induction of sexual reproduction. The identification of putative master regulators of gametogenesis provides a starting point for further functional characterization.

scholarly journals Understanding the Integrated Pathways and Mechanisms of Transporters, Protein Kinases, and Transcription Factors in Plants under Salt Stress

2021 ◽  
Vol 2021 ◽  
pp. 1-16
Author(s):  
Wasifa Hafiz Shah ◽  
Aadil Rasool ◽  
Seerat Saleem ◽  
Naveed Ul Mushtaq ◽  
Inayatullah Tahir ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Salt Stress ◽  
Protein Kinases ◽  
Stress Responses ◽  
Crop Improvement ◽  
Ion Homeostasis ◽  
Underlying Mechanism ◽  
Regulatory Proteins ◽  
Stress Signalling

Abiotic stress is the major threat confronted by modern-day agriculture. Salinity is one of the major abiotic stresses that influence geographical distribution, survival, and productivity of various crops across the globe. Plants perceive salt stress cues and communicate specific signals, which lead to the initiation of defence response against it. Stress signalling involves the transporters, which are critical for water transport and ion homeostasis. Various cytoplasmic components like calcium and kinases are critical for any type of signalling within the cell which elicits molecular responses. Stress signalling instils regulatory proteins and transcription factors (TFs), which induce stress-responsive genes. In this review, we discuss the role of ion transporters, protein kinases, and TFs in plants to overcome the salt stress. Understanding stress responses by components collectively will enhance our ability in understanding the underlying mechanism, which could be utilized for crop improvement strategies for achieving food security.

scholarly journals Use of fusion transcription factors to reprogram cellulase transcription and enable efficient cellulase production in Trichoderma reesei

2019 ◽  
Vol 12 (1) ◽  
Author(s):  
Fangzhong Wang ◽  
Ruiqin Zhang ◽  
Lijuan Han ◽  
Wei Guo ◽  
Zhiqiang Du ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Trichoderma Reesei ◽  
Parent Strain ◽  
Fungal Growth ◽  
Biomass Accumulation ◽  
Hyphal Growth ◽  
Fold Increase ◽  
Cellulase Production ◽  
Fungal Species ◽  
New Strategy

Abstract Background Trichoderma reesei is widely used for cellulase production and accepted as an example for cellulase research. Cre1-mediated carbon catabolite repression (CCR) can significantly inhibit the transcription of cellulase genes during cellulase fermentation in T. reesei. Early efforts have been undertaken to modify Cre1 for the release of CCR; however, this approach leads to arrested hyphal growth and decreased biomass accumulation, which negatively affects cellulase production. Results In this study, novel fusion transcription factors (fTFs) were designed to release or attenuate CCR inhibition in cellulase transcription, while Cre1 was left intact to maintain normal hyphal growth. Four designed fTFs were introduced into the T. reesei genome, which generated several transformants, named Kuace3, Kuclr2, Kuace2, and Kuxyr1. No obvious differences in growth were observed between the parent and transformant strains. However, the transcription levels of cel7a, a major cellulase gene, were significantly elevated in all the transformants, particularly in Kuace2 and Kuxyr1, when grown on lactose as a carbon source. This suggested that CCR inhibition was released or attenuated in the transformant strains. The growth of Kuace2 and Kuxyr1 was approximately equivalent to that of the parent strain in fed-batch fermentation process. However, we observed a 3.2- and 2.1-fold increase in the pNPCase titers of the Kuace2 and Kuxyr1 strains, respectively, compared with that of the parent strain. Moreover, we observed a 6.1- and 3.9-fold increase in the pNPCase titers of the Kuace2 and Kuxyr1 strains, respectively, compared with that of Δcre1 strain. Conclusions A new strategy based on fTFs was successfully established in T. reesei to improve cellulase titers without impairing fungal growth. This study will be valuable for lignocellulosic biorefining and for guiding the development of engineering strategies for producing other important biochemical compounds in fungal species.

scholarly journals In Silico Identification and Expression Analysis of Nuclear Factor Y (Nf-Y) Transcription Factors in Cucumber

Agronomy ◽  
2020 ◽  
Vol 10 (2) ◽  
pp. 236 ◽  
Author(s):  
Lianghai Chen ◽  
Yong Zhou ◽  
Wei Lai ◽  
Lifang Hu ◽  
Lunwei Jiang ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Crop Improvement ◽  
Nuclear Factor ◽  
Rna Seq ◽  
Abiotic Stress Response ◽  
Promoter Regions ◽  
Nuclear Factor Y ◽  
Cucumber Genome ◽  
Drought And Salt Stress ◽  
Gene Structures

The nuclear factor Y (NF-Y) transcription factors (TFs) play vital regulatory roles in diverse developmental processes and responses to abiotic stresses in plants. However, the NF-Y genes remain largely unknown in cucumber. In this study, based on phylogenetic and protein structure analyses, we identified 27 CsaNF-Y members of this gene family in the cucumber genome, including 7 NF-YAs, 13 NF-YBs, and 7 NF-YCs. Their chromosome locations, gene structures, conserved domains, gene duplication, and promoter regions containing stress- and hormone-responsive cis-elements were also analyzed. As reported earlier, RNA-seq data showed that the expression of some CsaNF-Y genes was tissue-specific and varied during fruit development. The qRT-PCR results showed that all the detected CsaNF-Y genes were differentially regulated by drought and salt stress. Taken together, our findings provide a comprehensive understanding of CsaNF-Y genes in the development and abiotic stress response of cucumber and lay the foundation for future crop improvement.

Coping with Drought and Salinity Stresses: Role of Transcription Factors in Crop Improvement

2013 ◽  
pp. 641-684 ◽  
Author(s):  
Karina F. Ribichich ◽  
Agustín L. Arce ◽  
Raquel Lía Chan
Keyword(s):  
Transcription Factors ◽  
Crop Improvement

Transcription Factors in Abiotic Stress Responses: Their Potentials in Crop Improvement

2014 ◽  
pp. 337-366 ◽  
Author(s):  
Xuan Lan Thi Hoang ◽  
Nguyen Binh Anh Thu ◽  
Nguyen Phuong Thao ◽  
Lam-Son Phan Tran
Keyword(s):  
Transcription Factors ◽  
Abiotic Stress ◽  
Stress Responses ◽  
Crop Improvement

scholarly journals Dissecting the Role of Promoters of Pathogen-sensitive Genes in Plant Defense

2020 ◽  
Vol 21 (7) ◽  
pp. 491-503
Author(s):  
Indrani Baruah ◽  
Gajendra Mohan Baldodiya ◽  
Jagajjit Sahu ◽  
Geetanjali Baruah
Keyword(s):  
Transcription Factors ◽  
Plant Resistance ◽  
Gene Networks ◽  
Crop Improvement ◽  
Regulatory Elements ◽  
Promoter Elements ◽  
New Genes ◽  
Pathogen Attack ◽  
Pathogen Response ◽  
Molecular Aspects

Plants inherently show resistance to pathogen attack but are susceptible to multiple bacteria, viruses, fungi, and phytoplasmas. Diseases as a result of such infection leads to the deterioration of crop yield. Several pathogen-sensitive gene activities, promoters of such genes, associated transcription factors, and promoter elements responsible for crosstalk between the defense signaling pathways are involved in plant resistance towards a pathogen. Still, only a handful of genes and their promoters related to plant resistance have been identified to date. Such pathogen-sensitive promoters are accountable for elevating the transcriptional activity of certain genes in response to infection. Also, a suitable promoter is a key to devising successful crop improvement strategies as it ensures the optimum expression of the required transgene. The study of the promoters also helps in mining more details about the transcription factors controlling their activities and helps to unveil the involvement of new genes in the pathogen response. Therefore, the only way out to formulate new solutions is by analyzing the molecular aspects of these promoters in detail. In this review, we provided an overview of the promoter motifs and cis-regulatory elements having specific roles in pathogen attack response. To elaborate on the importance and get a vivid picture of the pathogen-sensitive promoter sequences, the key motifs and promoter elements were analyzed with the help of PlantCare and interpreted with available literature. This review intends to provide useful information for reconstructing the gene networks underlying the resistance of plants against pathogens.

scholarly journals Transcription Factors Associated with Abiotic and Biotic Stress Tolerance and Their Potential for Crops Improvement

Genes ◽  
2019 ◽  
Vol 10 (10) ◽  
pp. 771 ◽  
Author(s):  
Baillo ◽  
Kimotho ◽  
Zhang ◽  
Xu
Keyword(s):  
Transcription Factors ◽  
Stress Tolerance ◽  
Stress Responses ◽  
Biotic Stress ◽  
Crop Improvement ◽  
Abiotic And Biotic Stress ◽  
Crop Species ◽  
Biotic Stresses ◽  
Wide Range ◽  
Tf Gene

In field conditions, crops are adversely affected by a wide range of abiotic stresses including drought, cold, salt, and heat, as well as biotic stresses including pests and pathogens. These stresses can have a marked effect on crop yield. The present and future effects of climate change necessitate the improvement of crop stress tolerance. Plants have evolved sophisticated stress response strategies, and genes that encode transcription factors (TFs) that are master regulators of stress-responsive genes are excellent candidates for crop improvement. Related examples in recent studies include TF gene modulation and overexpression approaches in crop species to enhance stress tolerance. However, much remains to be discovered about the diverse plant TFs. Of the >80 TF families, only a few, such as NAC, MYB, WRKY, bZIP, and ERF/DREB, with vital roles in abiotic and biotic stress responses have been intensively studied. Moreover, although significant progress has been made in deciphering the roles of TFs in important cereal crops, fewer TF genes have been elucidated in sorghum. As a model drought-tolerant crop, sorghum research warrants further focus. This review summarizes recent progress on major TF families associated with abiotic and biotic stress tolerance and their potential for crop improvement, particularly in sorghum. Other TF families and non-coding RNAs that regulate gene expression are discussed briefly. Despite the emphasis on sorghum, numerous examples from wheat, rice, maize, and barley are included. Collectively, the aim of this review is to illustrate the potential application of TF genes for stress tolerance improvement and the engineering of resistant crops, with an emphasis on sorghum.

scholarly journals Decoding neuronal diversity by single-cell Convert-seq

2019 ◽  
Author(s):  
Joachim Luginbühl ◽  
Tsukasa Kouno ◽  
Rei Nakano ◽  
Thomas E Chater ◽  
Divya M Sivaraman ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Single Cell ◽  
Regulatory Networks ◽  
Developmental Trajectories ◽  
Single Cells ◽  
Human Fibroblasts ◽  
Neuronal Diversity ◽  
Cell Fates ◽  
New Strategy ◽  
Research Challenge

SummaryThe conversion of cell fates is controlled by hierarchical gene regulatory networks (GRNs) that induce remarkable alterations in cellular and transcriptome states. The identification of key regulators within these networks from myriad of candidate genes, however, poses a major research challenge. Here we present Convert-seq, combining single-cell RNA sequencing (scRNA-seq) and pooled ectopic gene expression with a new strategy to discriminate sequencing reads derived from exogenous and endogenous transcripts. We demonstrate Convert-seq by associating hundreds of single cells during reprogramming of human fibroblasts to induced neurons (iN) with exogenous and endogenous transcriptional signatures. Convert-seq identified GRNs modulating the emergence of developmental trajectories and predicted combinatorial activation of exogenous transcription factors controlling iN subtype specification. Functional validation of iN subtypes generated by novel combinations of exogenous transcription factors establish Convert-seq as a broadly applicable workflow to rapidly identify key transcription factors and GRNs orchestrating the reprogramming of virtually any cell type.

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